Signac: seqinfo-methods – R documentation

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Documentation

Signac

seqinfo-methods

Access and modify sequence information for ChromatinAssay objects

Description

Methods for accessing and modifying Seqinfo object information stored in a ChromatinAssay object.

Usage

## S4 method for signature 'ChromatinAssay'
seqinfo(x)

## S4 replacement method for signature 'ChromatinAssay'
seqinfo(x) <- value

## S4 method for signature 'ChromatinAssay'
seqlevels(x)

## S4 replacement method for signature 'ChromatinAssay'
seqlevels(x) <- value

## S4 method for signature 'ChromatinAssay'
seqnames(x)

## S4 replacement method for signature 'ChromatinAssay'
seqnames(x) <- value

## S4 method for signature 'ChromatinAssay'
seqlengths(x)

## S4 replacement method for signature 'ChromatinAssay'
seqlengths(x) <- value

## S4 method for signature 'ChromatinAssay'
genome(x)

## S4 replacement method for signature 'ChromatinAssay'
genome(x) <- value

## S4 method for signature 'ChromatinAssay'
isCircular(x)

## S4 replacement method for signature 'ChromatinAssay'
isCircular(x) <- value

## S4 method for signature 'Seurat'
seqinfo(x)

## S4 replacement method for signature 'Seurat'
seqinfo(x) <- value

## S4 method for signature 'Seurat'
seqlevels(x)

## S4 replacement method for signature 'Seurat'
seqlevels(x) <- value

## S4 method for signature 'Seurat'
seqnames(x)

## S4 replacement method for signature 'Seurat'
seqnames(x) <- value

## S4 method for signature 'Seurat'
seqlengths(x)

## S4 replacement method for signature 'Seurat'
seqlengths(x) <- value

## S4 method for signature 'Seurat'
genome(x)

## S4 replacement method for signature 'Seurat'
genome(x) <- value

## S4 method for signature 'Seurat'
isCircular(x)

## S4 replacement method for signature 'Seurat'
isCircular(x) <- value

Arguments

`x`	A `ChromatinAssay` object
`value`	A `Seqinfo` object or name of a UCSC genome to store in the `ChromatinAssay`

Functions

seqinfo<-,ChromatinAssay-method: set method for ChromatinAssay objects
seqlevels,ChromatinAssay-method: get method for ChromatinAssay objects
seqlevels<-,ChromatinAssay-method: set method for ChromatinAssay objects
seqnames,ChromatinAssay-method: get method for ChromatinAssay objects
seqnames<-,ChromatinAssay-method: set method for ChromatinAssay objects
seqlengths,ChromatinAssay-method: get method for ChromatinAssay objects
seqlengths<-,ChromatinAssay-method: set method for ChromatinAssay objects
genome,ChromatinAssay-method: get method for ChromatinAssay objects
genome<-,ChromatinAssay-method: set method for ChromatinAssay objects
isCircular,ChromatinAssay-method: get method for ChromatinAssay objects
isCircular<-,ChromatinAssay-method: set method for ChromatinAssay objects
seqinfo,Seurat-method: get method for Seurat objects
seqinfo<-,Seurat-method: set method for Seurat objects
seqlevels,Seurat-method: get method for Seurat objects
seqlevels<-,Seurat-method: set method for Seurat objects
seqnames,Seurat-method: get method for Seurat objects
seqnames<-,Seurat-method: set method for Seurat objects
seqlengths,Seurat-method: get method for Seurat objects
seqlengths<-,Seurat-method: set method for Seurat objects
genome,Seurat-method: get method for Seurat objects
genome<-,Seurat-method: set method for Seurat objects
isCircular,Seurat-method: get method for Seurat objects
isCircular<-,Seurat-method: set method for Seurat objects